MolNFT v1 · #21979 · protein
Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 ångströms resolution
1SRD · COPPER,ZINC superoxide dismutase: “Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 ångströms resolution”. X-ray diffraction, 2 ligands (CU, ZN), 5 pockets (best druggability 0.72). MolNFT v1 #21979 on…
- PDB
- 1SRD
- Type
- protein
- Length
- 616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COPPER,ZINC superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P07505
- Ligands
- CU, ZN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | COPPER,ZINC superoxide dismutase (EC 1.15.1.1) | protein | 154 | 3% helix, 36% strand | P07505 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.72 | 0.78 | 54 | empty |
| 2 | 177 | 0.59 | 0.82 | 37 | empty |
| 3 | 161 | 0.58 | 0.83 | 30 | empty |
| 4 | 179 | 0.44 | 0.74 | 28 | empty |
| 5 | 107 | 0.34 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 715 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 694 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 363 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1SRD · Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 Angstroms… · the same entry in another collection · chain A against A, TM-score 1.00
- P07505 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn], chloroplastic (P07505) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07505
- Elsewhere: RCSB PDB 1SRD · PDBe 1SRD · UniProt P07505
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